2002 K1200LT easy to start and good idle but bad misfire above idle, not drivable

My 2002 K1200LT has developed a terrible misfire at all speed greater than idle both steady state and no load acceleration. The engine starts easily cold and hot and idles evenly. No black smoke out exhaust but plugs are a little sooty.
I have checked all wiring connections, installed new air filter, added new tank of fuel. Changed the fuel tank pump and filter a few years ago. The only recent mechanical change was removed and installed a new aftermarket muffler. I have run with the new muffler off (open exhaust after catalyst) with no change in misfire problem.
Any suggestions?
Tim
Tucson, AZ

Valve adjustment.

Plug wires. (After fresh plugs)

One thing at a time too.

Charlie

Check for chafing on the spark plug wires they rub the head in several spots.

It sounds like a mostly clogged fuel filter to me, possibly caused by water in the fuel. At about $3 a bottle of Isoheet in the red bottle is worth a shot.

The timing and order of what you did is important, and (to me) a bit unclear.
Are you saying that without the muffler installed, the problem goes away? If that's the case, the problem obviously lies somewhere within the muffler itself.
If that test was run prior to the problem occurring, then the options are more numerous.

Exhaust systems matter a lot to low-end performance. Your saying that with your new aftermarket muffler the bike behaves as if there is no muffler (runs poorly either way). I’d try putting your old pipe back on.

Welcome to the forum! Hope you get the bike back on the road soon!

How did the replacement exhaust accommodate the OEM oxygen sensor? Any chance this might be the problem?